Urxvt can have problems with the spacings of some fonts (eg Terminus), an option has been introduced in the latest version (9.07), allowing you to manually tweak the spacings, unfortunately this isn't in the repositories, it is however in the Debian sid repos http://packages.debian.org/sid/i386/rxvt-unicode/download.
to install the downloaded .deb:

sudo dpkg --force-depends-version -i /path/to/urxvt.deb

You need to use dpkg as the dependencies include newer versions of things not available in the repos, it works fine with CrunchBang 9.04, so i suspect its an issue of Debian playing safe will dependency versions.

Then you can add the following to your .Xdefaults:

URxvt*letterSpace: -1

Where -1 decreases the spacing by one pixel, but can be adjusted as needed.

To enable true transparency first you need to enable a compositing manager, xcompmgr just happens to be installed by default, this can be enabled from the main menu → Preferences → compositing → enable compositing or alternatively to have it start automatically uncomment the entry in your ~/.config/openbox/autostart.sh file.

then to modify your .Xdefaults file, first change the background line to add the opacity:

The colours are the same as those already defined in your .Xdefaults, tabs can be created by pressing <shift>-down or clicking on 'NEW', and can by cycled through using <shift>-left and <shift>-right, or clicking on the relevant tabs.

There is also a script for GTK tabs here Z-Edit VARIOUS rxvt-tabbed [OK?], it doesn't seem to have any keybindings that i can find but you may find it useful.
(Note: I think its standard in Arch, and comes with the source file, just not Debian or Ubuntu, so you may already have this installed)

It is possible to set up Urxvt so that a single Daemon runs, and individual client windows connect to it, (urxvtd and urxvtc), the advantage of this is reduced memory usage, although a crash would affect all windows.